How has a visual novel gotten a shortened title that shares no words or abbreviations with its original name?
Visual Novel? No idea. Light novel? Boku wa (written as ha) tomodachi ga sukunai. Yes, it's as stupid as it sounds.
The galgames described in Haganai seem to have some actual value for learning how to treat people. So how come Sena, who's become an expert at them, isn't any better at making friends?
She doesn't seem to treat anyone around her, with the exception of the Hasegawa siblings, as being worth her time. In addition, she's dealing with real people, not characters who automatically become nicer/more affectionate when the right "flags" are raised.
Kodaka catches hell in part for having blonde hair. Kobato and Sena get a free pass?
His hair is a less appealing shade of blonde, and the brown patches/highlights make it look like he did it himself with a peroxide kit (i.e, delinquent).
Why doesn't he..... this is just a suggestion..... change... his hair color??
It's the only memento of his mother. He doesn't want to betray her, since he loves her more than he hates his life.
The biggest issue for him is not that he has blonde hair, its that he has blonde hair and an Asian face. With Sena and Kobato, they actually look European (at least, European enough), so them having blonde hair? Whatever, they aren't/don't seem to be Japanese. Kodaka on the other hand looks like a Japanese guy with blonde hair, and not Golden Blonde (which is what many people, especially in places where blonde is not common presume to be "real" blonde), he has dirty blonde hair (somewhere between brown and yellow, leaning towards yellow, sometimes with highlights and lowlights) i.e. obviously dyed, at least to the Japanese mind (according to the stereotype anyway). And who is the only group of Japanese people who commonly dye their hair yellow (again, according to the stereotype)? Delinquents.
What about Yozora? Analyzing her behavior, she originally dresses in boys' clothes and generally acts boy-like. She is too embarrassed to be seen in girls' clothes by her friend Taka. She doesn't get along with any of the girls in her classes, feeling like an outsider to their world, to the point where she has long hair simply because she can't handle being in a hair salon where other girls are chatting and gossiping and otherwise being girly. When it is pointed out to her that the "boyish" clothes she picks out aren't actually intended to make girls look like boys, she gives away the clothes, buys a tracksuit, and leaves in embarrassment. Further, she jumps on the concept of yaoi, and makes a couple tentative passes at Kodaka after this revelation.
Just spit-balling, but while Yuki is a ... weird and highly arguable case, I believe that Yozora is more likely to be a Tom Boy with a bit of a crappy track record with other girls than anything else. If her only constructive relationship since childhood was with a boy and she had any number of bad experiences with girls, it's pretty easy to see how she could develop a boys=good, girls=bad mentality.